Abstract Background Mediastinal lymph node dissection (LND) is a critical factor to decide the surgical strategy for Esophagogastric junction (EGJ) cancers. As a result of a prospective multicenter study in Japan, surgical algorithm including the extent of LND for EGJ cancers has recently been proposed according to the length of esophageal invasion. However, preoperative measure predicting upper mediastinal LN metastasis is still lacking, and the oncologic efficacy of mediastinal LND remain unknown. Methods The aim of this study was to identify preoperative factors predicting mediastinal LN metastasis, and we hypothesized that preoperative CT image would be of utility. Patients who underwent surgical treatment for Siewert Type I/II EGJ cancer with esophageal invasion with curative intent between 2000 and 2022 at the Tokai University Hospital were retrospectively reviewed. Results A total of 103 patients were enrolled. Among them, 55, 74, and 74 patients underwent upper, middle, and lower mediastinal LND, respectively. Upper/middle/lower mediastinal LN metastasis was observed in 14/13/23 of those patients, respectively, with lower thoracic paraesophageal LNs (29%), middle thoracic paraesophageal LNs (18%), and right recurrent nerve LNs (16%) being the three most common metastatic sites. Estimated invasion depth of the primary lesion≧cT3 (p≦0.007), tumor size≧4cm (p≦0.002), esophageal invasion length≧4cm (p≦0.007) and minor axis of the LN≧5mm by preoperative CT image (p<0.001) were significant preoperative factors related to mediastinal LN metastasis. Conclusion Clinical T factor, tumor size, the size of mediastinal LN by CT image, as well as esophageal invasion length, were important preoperative factors to predict mediastinal LN metastasis, and those factors should be taken into consideration to decide the surgical strategy for EGJ cancers with esophageal invasion. Survival impact of mediastinal LND still remain unclear, and further accumulation of cases and prospective studies are awaited.